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Simplied getAttributeAsX interfaces 

-- Removed versions getAttribriteAsX(key) that except on not having the value.
-- Removed version that getAttributeAsXNoException(key)
-- The only available assessors are now getAttributeAsX(key, default).
-- This single accessors properly handle their argument types, so if the value is a double it is returned directly for getAttributeAsDouble(), or if it's a string it's converted to a double.  If the key isn't found, default is returned.
This commit is contained in:
Mark DePristo 2011-09-02 12:27:11 -04:00
parent c57198a1b9
commit 82f2131777
21 changed files with 79 additions and 80 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SBByDepth.java
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@ -26,7 +26,7 @@ public class SBByDepth extends AnnotationByDepth {
if (!vc.hasAttribute(VCFConstants.STRAND_BIAS_KEY))
return null;
double sBias = Double.valueOf(vc.getAttributeAsString(VCFConstants.STRAND_BIAS_KEY));
double sBias = vc.getAttributeAsDouble(VCFConstants.STRAND_BIAS_KEY, -1);
final Map<String, Genotype> genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() == 0 )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
View File

@ -73,7 +73,7 @@ public class HaplotypeIndelErrorModel {
baseMatchArray = new double[MAX_CACHED_QUAL+1];
baseMismatchArray = new double[MAX_CACHED_QUAL+1];
for (int k=1; k <= MAX_CACHED_QUAL; k++) {
double baseProb = QualityUtils.qualToProb(k);
double baseProb = QualityUtils.qualToProb((byte)k);
baseMatchArray[k] = probToQual(baseProb);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
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@ -37,7 +37,7 @@ public class PhasingRead extends BaseArray {
public PhasingRead(int length, int mappingQual) {
super(length);
this.mappingProb = new PreciseNonNegativeDouble(QualityUtils.qualToProb(mappingQual));
this.mappingProb = new PreciseNonNegativeDouble(QualityUtils.qualToProb((byte)mappingQual));
this.baseProbs = new PreciseNonNegativeDouble[length];
Arrays.fill(this.baseProbs, null);

10
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
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@ -44,12 +44,12 @@ public class RefSeqDataParser {
String nameKeyToUseMultiplePrefix = nameKeyToUse + "_";
Map<String, String> entriesToNames = new HashMap<String, String>();
Integer numRecords = vc.getAttributeAsIntegerNoException(NUM_RECORDS_KEY);
if (numRecords != null) {
int numRecords = vc.getAttributeAsInt(NUM_RECORDS_KEY, -1);
if (numRecords != -1) {
boolean done = false;
if (numRecords == 1) { // Check if perhaps the single record doesn't end with "_1":
String name = vc.getAttributeAsStringNoException(nameKeyToUse);
String name = vc.getAttributeAsString(nameKeyToUse, null);
if (name != null) {
entriesToNames.put(nameKeyToUse, name);
done = true;
@ -59,14 +59,14 @@ public class RefSeqDataParser {
if (!done) {
for (int i = 1; i <= numRecords; i++) {
String key = nameKeyToUseMultiplePrefix + i;
String name = vc.getAttributeAsStringNoException(key);
String name = vc.getAttributeAsString(key, null);
if (name != null)
entriesToNames.put(key, name);
}
}
}
else { // no entry with the # of records:
String name = vc.getAttributeAsStringNoException(nameKeyToUse);
String name = vc.getAttributeAsString(nameKeyToUse, null);
if (name != null) {
entriesToNames.put(nameKeyToUse, name);
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -109,12 +109,12 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
case SNP:
nVariantLoci++;
nSNPs++;
if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
if (vc1.getAttributeAsBoolean("ISSINGLETON", false)) nSingletons++;
break;
case MNP:
nVariantLoci++;
nMNPs++;
if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
if (vc1.getAttributeAsBoolean("ISSINGLETON", false)) nSingletons++;
break;
case INDEL:
nVariantLoci++;
@ -136,7 +136,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
String refStr = vc1.getReference().getBaseString().toUpperCase();
String aaStr = vc1.hasAttribute("ANCESTRALALLELE") ? vc1.getAttributeAsString("ANCESTRALALLELE").toUpperCase() : null;
String aaStr = vc1.hasAttribute("ANCESTRALALLELE") ? vc1.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase() : null;
// if (aaStr.equals(".")) {
// aaStr = refStr;
// }

3
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
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@ -219,7 +219,8 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
}
public static Double getPQ(Genotype gt) {
return gt.getAttributeAsDoubleNoException(ReadBackedPhasingWalker.PQ_KEY);
Double d = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1);
return d == -1 ? null : d;
}
public static boolean topMatchesTop(AllelePair b1, AllelePair b2) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
View File

@ -120,7 +120,7 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval
if ( eval.hasGenotypes() )
ac = eval.getChromosomeCount(eval.getAlternateAllele(0));
else if ( eval.hasAttribute("AC") ) {
ac = Integer.valueOf(eval.getAttributeAsString("AC"));
ac = eval.getAttributeAsInt("AC", -1);
}
if ( ac != -1 ) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
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@ -50,7 +50,7 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv
}
String refStr = vc.getReference().getBaseString().toUpperCase();
String aaStr = vc.getAttributeAsString("ANCESTRALALLELE").toUpperCase();
String aaStr = vc.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase();
if (aaStr != null && !aaStr.equalsIgnoreCase("null") && !aaStr.equals(".")) {
BaseUtils.BaseSubstitutionType aaSubType = BaseUtils.SNPSubstitutionType(aaStr.getBytes()[0], vc.getAlternateAllele(0).getBases()[0]);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
View File

@ -130,7 +130,7 @@ public class ValidationReport extends VariantEvaluator implements StandardEval {
//// System.out.printf(" ac = %d%n", ac);
}
else
ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY);
ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO;
} else if ( vc.hasGenotypes() ) {
return vc.isPolymorphic() ? SiteStatus.POLY : SiteStatus.MONO;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
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@ -45,7 +45,7 @@ public class AlleleCount extends VariantStratifier {
if (eval != null) {
int AC = -1;
if ( eval.hasAttribute("AC") && eval.getAttribute("AC") instanceof Integer ) {
AC = eval.getAttributeAsInt("AC");
AC = eval.getAttributeAsInt("AC", 0);
} else if ( eval.isVariant() ) {
for (Allele allele : eval.getAlternateAlleles())
AC = Math.max(AC, eval.getChromosomeCount(allele));

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
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@ -28,7 +28,7 @@ public class AlleleFrequency extends VariantStratifier {
if (eval != null) {
try {
relevantStates.add(String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF") / 5.0, 3))));
relevantStates.add(String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3))));
} catch (Exception e) {
return relevantStates;
}

10
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
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@ -92,8 +92,8 @@ public class Degeneracy extends VariantStratifier {
Integer frame = null;
if (eval.hasAttribute("refseq.functionalClass")) {
aa = eval.getAttributeAsString("refseq.variantAA");
frame = eval.getAttributeAsInt("refseq.frame");
aa = eval.getAttributeAsString("refseq.variantAA", null);
frame = eval.getAttributeAsInt("refseq.frame", 0);
} else if (eval.hasAttribute("refseq.functionalClass_1")) {
int annotationId = 1;
String key;
@ -101,7 +101,7 @@ public class Degeneracy extends VariantStratifier {
do {
key = String.format("refseq.functionalClass_%d", annotationId);
String newtype = eval.getAttributeAsString(key);
String newtype = eval.getAttributeAsString(key, null);
if ( newtype != null &&
( type == null ||
@ -111,13 +111,13 @@ public class Degeneracy extends VariantStratifier {
type = newtype;
String aakey = String.format("refseq.variantAA_%d", annotationId);
aa = eval.getAttributeAsString(aakey);
aa = eval.getAttributeAsString(aakey, null);
if (aa != null) {
String framekey = String.format("refseq.frame_%d", annotationId);
if (eval.hasAttribute(framekey)) {
frame = eval.getAttributeAsInt(framekey);
frame = eval.getAttributeAsInt(framekey, 0);
}
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
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@ -32,7 +32,7 @@ public class FunctionalClass extends VariantStratifier {
String type = null;
if (eval.hasAttribute("refseq.functionalClass")) {
type = eval.getAttributeAsString("refseq.functionalClass");
type = eval.getAttributeAsString("refseq.functionalClass", null);
} else if (eval.hasAttribute("refseq.functionalClass_1")) {
int annotationId = 1;
String key;
@ -40,7 +40,7 @@ public class FunctionalClass extends VariantStratifier {
do {
key = String.format("refseq.functionalClass_%d", annotationId);
String newtype = eval.getAttributeAsString(key);
String newtype = eval.getAttributeAsString(key, null);
if ( newtype != null && !newtype.equalsIgnoreCase("null") &&
( type == null ||

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
View File

@ -115,7 +115,7 @@ public class VQSRCalibrationCurve {
if ( vc.isFiltered() )
return 0.0;
else if ( vc.hasAttribute(VQSRQualKey) ) {
double qual = vc.getAttributeAsDouble(VQSRQualKey);
double qual = vc.getAttributeAsDouble(VQSRQualKey, 0.0);
return probTrueVariant(qual);
} else {
throw new UserException.VariantContextMissingRequiredField(VQSRQualKey, vc);
@ -143,7 +143,7 @@ public class VQSRCalibrationCurve {
for ( int i = 0; i < log10Likelihoods.length; i++) {
double p = Math.pow(10, log10Likelihoods[i]);
double q = alpha * p + (1-alpha) * noInfoPr;
if ( DEBUG ) System.out.printf(" vqslod = %.2f, p = %.2e, alpha = %.2e, q = %.2e%n", vc.getAttributeAsDouble(VQSRQualKey), p, alpha, q);
if ( DEBUG ) System.out.printf(" vqslod = %.2f, p = %.2e, alpha = %.2e, q = %.2e%n", vc.getAttributeAsDouble(VQSRQualKey, 0.0), p, alpha, q);
updated[i] = Math.log10(q);
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -575,7 +575,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
// ok we have a comp VC and we need to match the AF spectrum of inputAFRodName.
// We then pick a variant with probablity AF*desiredFraction
if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY);
String afo = sub.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY, null);
double af;
double afBoost = 1.0;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -192,7 +192,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
if ( getters.containsKey(field) ) {
val = getters.get(field).get(vc);
} else if ( vc.hasAttribute(field) ) {
val = vc.getAttributeAsString(field);
val = vc.getAttributeAsString(field, null);
} else if ( isWildCard(field) ) {
Set<String> wildVals = new HashSet<String>();
for ( Map.Entry<String,Object> elt : vc.getAttributes().entrySet()) {

14
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
View File

@ -105,7 +105,10 @@ public class VCFCodec extends AbstractVCFCodec {
* @return a set of the filters applied or null if filters were not applied to the record (e.g. as per the missing value in a VCF)
*/
protected Set<String> parseFilters(String filterString) {
return parseFilters(filterHash, lineNo, filterString);
}
public static Set<String> parseFilters(final Map<String, LinkedHashSet<String>> cache, final int lineNo, final String filterString) {
// null for unfiltered
if ( filterString.equals(VCFConstants.UNFILTERED) )
return null;
@ -113,13 +116,13 @@ public class VCFCodec extends AbstractVCFCodec {
if ( filterString.equals(VCFConstants.PASSES_FILTERS_v4) )
return Collections.emptySet();
if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) )
generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4");
generateException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4", lineNo);
if ( filterString.length() == 0 )
generateException("The VCF specification requires a valid filter status");
generateException("The VCF specification requires a valid filter status", lineNo);
// do we have the filter string cached?
if ( filterHash.containsKey(filterString) )
return filterHash.get(filterString);
if ( cache != null && cache.containsKey(filterString) )
return Collections.unmodifiableSet(cache.get(filterString));
// empty set for passes filters
LinkedHashSet<String> fFields = new LinkedHashSet<String>();
@ -129,7 +132,8 @@ public class VCFCodec extends AbstractVCFCodec {
else
fFields.addAll(Arrays.asList(filterString.split(VCFConstants.FILTER_CODE_SEPARATOR)));
filterHash.put(filterString, fFields);
fFields = fFields;
if ( cache != null ) cache.put(filterString, fFields);
return Collections.unmodifiableSet(fFields);
}

9
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
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@ -293,17 +293,8 @@ public class Genotype {
return commonInfo.getAttribute(key, defaultValue);
}
public String getAttributeAsString(String key) { return commonInfo.getAttributeAsString(key); }
public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); }
public int getAttributeAsInt(String key) { return commonInfo.getAttributeAsInt(key); }
public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); }
public double getAttributeAsDouble(String key) { return commonInfo.getAttributeAsDouble(key); }
public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); }
public boolean getAttributeAsBoolean(String key) { return commonInfo.getAttributeAsBoolean(key); }
public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
public Integer getAttributeAsIntegerNoException(String key) { return commonInfo.getAttributeAsIntegerNoException(key); }
public Double getAttributeAsDoubleNoException(String key) { return commonInfo.getAttributeAsDoubleNoException(key); }
public String getAttributeAsStringNoException(String key) { return commonInfo.getAttributeAsStringNoException(key); }
public Boolean getAttributeAsBooleanNoException(String key) { return commonInfo.getAttributeAsBooleanNoException(key); }
}

53
public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java
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@ -204,27 +204,40 @@ public final class InferredGeneticContext {
return defaultValue;
}
// public AttributedObject getAttributes(Collection<Object> keys) {
// AttributedObject selected = new AttributedObject();
//
// for ( Object key : keys )
// selected.putAttribute(key, this.getAttribute(key));
//
// return selected;
// }
public String getAttributeAsString(String key, String defaultValue) {
Object x = getAttribute(key);
if ( x == null ) return defaultValue;
if ( x instanceof String ) return (String)x;
return String.valueOf(x); // throws an exception if this isn't a string
}
public String getAttributeAsString(String key) { return (String.valueOf(getAttribute(key))); } // **NOTE**: will turn a null Object into the String "null"
public int getAttributeAsInt(String key) { Object x = getAttribute(key); return x instanceof Integer ? (Integer)x : Integer.valueOf((String)x); }
public double getAttributeAsDouble(String key) { Object x = getAttribute(key); return x instanceof Double ? (Double)x : Double.valueOf((String)x); }
public boolean getAttributeAsBoolean(String key) { Object x = getAttribute(key); return x instanceof Boolean ? (Boolean)x : Boolean.valueOf((String)x); }
public int getAttributeAsInt(String key, int defaultValue) {
Object x = getAttribute(key);
if ( x == null ) return defaultValue;
if ( x instanceof Integer ) return (Integer)x;
return Integer.valueOf((String)x); // throws an exception if this isn't a string
}
public String getAttributeAsString(String key, String defaultValue) { return (String)getAttribute(key, defaultValue); }
public int getAttributeAsInt(String key, int defaultValue) { return (Integer)getAttribute(key, defaultValue); }
public double getAttributeAsDouble(String key, double defaultValue) { return (Double)getAttribute(key, defaultValue); }
public boolean getAttributeAsBoolean(String key, boolean defaultValue){ return (Boolean)getAttribute(key, defaultValue); }
public double getAttributeAsDouble(String key, double defaultValue) {
Object x = getAttribute(key);
if ( x == null ) return defaultValue;
if ( x instanceof Double ) return (Double)x;
return Double.valueOf((String)x); // throws an exception if this isn't a string
}
public Integer getAttributeAsIntegerNoException(String key) { try {return getAttributeAsInt(key);} catch (Exception e) {return null;} }
public Double getAttributeAsDoubleNoException(String key) { try {return getAttributeAsDouble(key);} catch (Exception e) {return null;} }
public String getAttributeAsStringNoException(String key) { if (getAttribute(key) == null) return null; return getAttributeAsString(key); }
public Boolean getAttributeAsBooleanNoException(String key) { try {return getAttributeAsBoolean(key);} catch (Exception e) {return null;} }
public boolean getAttributeAsBoolean(String key, boolean defaultValue) {
Object x = getAttribute(key);
if ( x == null ) return defaultValue;
if ( x instanceof Boolean ) return (Boolean)x;
return Boolean.valueOf((String)x); // throws an exception if this isn't a string
}
// public String getAttributeAsString(String key) { return (String.valueOf(getAttribute(key))); } // **NOTE**: will turn a null Object into the String "null"
// public int getAttributeAsInt(String key) { Object x = getAttribute(key); return x instanceof Integer ? (Integer)x : Integer.valueOf((String)x); }
// public double getAttributeAsDouble(String key) { Object x = getAttribute(key); return x instanceof Double ? (Double)x : Double.valueOf((String)x); }
// public boolean getAttributeAsBoolean(String key) { Object x = getAttribute(key); return x instanceof Boolean ? (Boolean)x : Boolean.valueOf((String)x); }
// public Integer getAttributeAsIntegerNoException(String key) { try {return getAttributeAsInt(key);} catch (Exception e) {return null;} }
// public Double getAttributeAsDoubleNoException(String key) { try {return getAttributeAsDouble(key);} catch (Exception e) {return null;} }
// public String getAttributeAsStringNoException(String key) { if (getAttribute(key) == null) return null; return getAttributeAsString(key); }
// public Boolean getAttributeAsBooleanNoException(String key) { try {return getAttributeAsBoolean(key);} catch (Exception e) {return null;} }
}

10
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -666,21 +666,11 @@ public class VariantContext implements Feature { // to enable tribble intergrati
return commonInfo.getAttribute(key, defaultValue);
}
public String getAttributeAsString(String key) { return commonInfo.getAttributeAsString(key); }
public String getAttributeAsString(String key, String defaultValue) { return commonInfo.getAttributeAsString(key, defaultValue); }
public int getAttributeAsInt(String key) { return commonInfo.getAttributeAsInt(key); }
public int getAttributeAsInt(String key, int defaultValue) { return commonInfo.getAttributeAsInt(key, defaultValue); }
public double getAttributeAsDouble(String key) { return commonInfo.getAttributeAsDouble(key); }
public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); }
public boolean getAttributeAsBoolean(String key) { return commonInfo.getAttributeAsBoolean(key); }
public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
public Integer getAttributeAsIntegerNoException(String key) { return commonInfo.getAttributeAsIntegerNoException(key); }
public Double getAttributeAsDoubleNoException(String key) { return commonInfo.getAttributeAsDoubleNoException(key); }
public String getAttributeAsStringNoException(String key) { return commonInfo.getAttributeAsStringNoException(key); }
public Boolean getAttributeAsBooleanNoException(String key) { return commonInfo.getAttributeAsBooleanNoException(key); }
// ---------------------------------------------------------------------------------------------------------
//
// Working with alleles

16
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -565,11 +565,11 @@ public class VariantContextUtils {
// special case DP (add it up) and ID (just preserve it)
//
if (vc.hasAttribute(VCFConstants.DEPTH_KEY))
depth += Integer.valueOf(vc.getAttributeAsString(VCFConstants.DEPTH_KEY));
depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
if (rsID == null && vc.hasID())
rsID = vc.getID();
if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY);
String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null);
// lets see if the string contains a , separator
if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) {
List<String> alleleCountArray = Arrays.asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1).split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR));
@ -1147,9 +1147,7 @@ public class VariantContextUtils {
for (String orAttrib : MERGE_OR_ATTRIBS) {
boolean attribVal = false;
for (VariantContext vc : vcList) {
Boolean val = vc.getAttributeAsBooleanNoException(orAttrib);
if (val != null)
attribVal = (attribVal || val);
attribVal = vc.getAttributeAsBoolean(orAttrib, false);
if (attribVal) // already true, so no reason to continue:
break;
}
@ -1159,7 +1157,7 @@ public class VariantContextUtils {
// Merge ID fields:
String iDVal = null;
for (VariantContext vc : vcList) {
String val = vc.getAttributeAsStringNoException(VariantContext.ID_KEY);
String val = vc.getAttributeAsString(VariantContext.ID_KEY, null);
if (val != null && !val.equals(VCFConstants.EMPTY_ID_FIELD)) {
if (iDVal == null)
iDVal = val;
@ -1239,8 +1237,10 @@ public class VariantContextUtils {
public PhaseAndQuality(Genotype gt) {
this.isPhased = gt.isPhased();
if (this.isPhased)
this.PQ = gt.getAttributeAsDoubleNoException(ReadBackedPhasingWalker.PQ_KEY);
if (this.isPhased) {
this.PQ = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1);
if ( this.PQ == -1 ) this.PQ = null;
}
}
}